Systems approach for the selection of micro-RNAs as therapeutic biomarkers of anti-EGFR monoclonal antibody treatment in colorectal cancer

Identification of Key mRNAs and Pathways in Colorectal Cancer

Colorectal cancer (CRC) is the third most cancer-related death worldwide. This work aimed to identify potential hub genes and dysregulated pathways in the CRC by bioinformatics analysis. Three gene expression datasets were collected from GEO datasets, including tumor sample (N = 242) and adjacent nontumor tissue sample (N = 59). RankProd was used to discover the differential expressed genes between tumor and adjacent nontumor tissues for datasets generated by different laboratories. The gene set enrichment analysis conducted on the DE genes, followed by the protein-protein interaction (PPI) network. In total, 2,007 significant differential expression (DE) genes between tumor and adjacent nontumor tissues, include 1,090 upregulated genes and 917 downregulated genes in the tumor. The DE mRNAs are involved in cancer-related pathways. We comprehensively identified the CRC-related key mRNAs. Our data demonstrated combined different resources of transcriptomes will promote the understanding of the molecular mechanisms underlying CRC development and may be useful in discovering candidate molecular biomarkers for diagnosing, prognosis, and treating of CRC.

Personalized medicine in colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease with various genetic and epigenetic factors leading to difficulties in response to both the therapy and drug resistance. Moreover, even in tumors with similar histopathological characteristics, different responses and molecular features could be observed because of the genetic basis and its interactions with the living environment. Through personalized medicine, we can classify patients into separate groups according to their genetic and epigenetic features and their susceptibility for a specific disease which could help with choosing the best therapeutic approach. In this review, genetic and epigenetic factors that cause heterogeneity in colorectal cancer are evaluated and proper drug administration in both chemotherapy and target therapy are suggested.

MicroR-545 mediates colorectal cancer cells proliferation through up-regulating epidermal growth factor receptor expression in HOTAIR long non-coding RNA dependent

The functional impact of recently discovered miRNAs in human cancer remains to be clarified. One miRNA in colorectal cancer which has attracted attention is miR-545. In this study, we examined the function of miR-545 in proliferation of colorectal cancer cells. Expressions of HOTAIR, miRNA-545, and epidermal growth factor receptor (EGFR) mRNA were measured in 100 paired cancerous and non-cancerous tissues as well as in SW480 and LOVO colorectal cancer cell (CRC) lines by quantitative RT-PCR. The relative protein level of EGFR was measured using western blotting. Effects of miRNA-545 and HOTAIR on gastric cancer cells were studied by overexpression and RNA interference approaches. Insight of mechanism of promotion cancer by miR-545 was gained from luciferase reporter assay and gene expression analysis. CRC proliferation was evaluated using clone formation and MTT assay. Differential expressions of HOTAIR, miR-545, and EGFR were observed in cancerous tissues in comparison to non-cancerous tissues. By expressional management of miR-545, we observed that miR-545 negatively regulated cell proliferation. Also luciferase reporter assay revealed that miR-545 inhibited regulated EGFR expression by affecting its 3'-UTR activity. In addition, miR-545 expression was suppressed by HOTAIR overexpression whereas enhanced by HOTAIR silence. Suppression of EGFR expression by miR-545 mimic was abrogated by HOTAIR overexpression. Monitoring of tumor growth in mice showed that miR-545 overexpression suppressed LOVO tumor growth. Our data suggested that HOTAIR long non-coding RNA mediates microR-545 regulating colorectal cancer cells proliferation.

Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods

MicroRNAs (miRs) are small single-stranded noncoding RNA that function in RNA silencing and post-transcriptional regulation of gene expression. An increasing number of studies have shown that miRs play an important role in tumorigenesis, and understanding the regulatory mechanism of miRs in this gene regulatory network will help elucidate the complex biological processes at play during malignancy. Despite advances, determination of miR–target interactions (MTIs) and identification of functional modules composed of miRs and their specific targets remain a challenge. A large amount of data generated by high-throughput methods from various sources are available to investigate MTIs. The development of data-driven tools to harness these multi-dimensional data has resulted in significant progress over the past decade. In parallel, large-scale cancer genomic projects are allowing new insights into the commonalities and disparities of miR–target regulation across cancers. In the first half of this review, we explore methods for identification of pairwise MTIs, and in the second half, we explore computational tools for discovery of miR-regulatory modules in a cancer-specific and pan-cancer context. We highlight strengths and limitations of each of these tools as a practical guide for the computational biologists.

Roles and mechanisms of action of microRNAs in colorectal cancer

MicroRNAs (miRNAs) are a class of endogenous, evolutionarily conserved small non-coding RNAs, which play a vital role in tumour formation, development, metastasis and recurrence by inducing DNA methylation, changing tumor microenvironment and regulating signal pathways such as Wnt/β-catenin, phosphoinositide3-kinase (PI3K), K-RAS, epithelial mesenchymal transitions (EMT) and so on. Recent studies have found that the expression of many miRNAs is dyregulated in colorectal cancer, and they participate in and control the formation and development of colorectal cancer. Thus, understanding the roles and mechanisms of action of miRNAs in colorectal cancer can provide a new avenue for its early diagnosis, clinical staging, treatment and prognosis evaluation.

MicroRNAs as Regulator of Signaling Networks in Metastatic Colon Cancer

MicroRNAs (miRNAs) are a class of small, noncoding RNA molecules capable of regulating gene expression translationally and/or transcriptionally. A large number of evidence have demonstrated that miRNAs have a functional role in both physiological and pathological processes by regulating the expression of their target genes. Recently, the functionalities of miRNAs in the initiation, progression, angiogenesis, metastasis, and chemoresistance of tumors have gained increasing attentions. Particularly, the alteration of miRNA profiles has been correlated with the transformation and metastasis of various cancers, including colon cancer. This paper reports the latest findings on miRNAs involved in different signaling networks leading to colon cancer metastasis, mainly focusing on miRNA profiling and their roles in PTEN/PI3K, EGFR, TGFβ, and p53 signaling pathways of metastatic colon cancer. The potential of miRNAs used as biomarkers in the diagnosis, prognosis, and therapeutic targets in colon cancer is also discussed.